Gromacs Py
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Gromacs_py
Installation
Gromacs_py
basic example
Gromacs simulation class
Topologie related class
Tools
Script
Gromacs Py
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A
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C
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D
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E
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F
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G
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I
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M
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P
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R
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S
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T
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W
A
add_ions() (gromacs_py.gromacs.gmx5.GmxSys method)
add_mdp() (gromacs_py.gromacs.gmx5.GmxSys method)
add_mol() (gromacs_py.gromacs.gmx5.TopSys method)
add_ndx() (gromacs_py.gromacs.gmx5.GmxSys method)
add_posre() (gromacs_py.gromacs.gmx5.TopSys method)
add_top() (gromacs_py.gromacs.gmx5.GmxSys method)
add_tpr() (gromacs_py.gromacs.gmx5.GmxSys method)
add_zinc_finger() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
atom_dist() (gromacs_py.gromacs.tools.pdb_manip.Coor static method)
C
center_of_mass() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
change_index_pdb_field() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
change_pdb_field() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
charge() (gromacs_py.gromacs.gmx5.TopSys method)
check_directory_exist() (in module gromacs_py.gromacs.tools.os_command)
check_file_and_create_path() (in module gromacs_py.gromacs.tools.os_command)
check_file_exist() (in module gromacs_py.gromacs.tools.os_command)
Command (class in gromacs_py.gromacs.tools.os_command)
compute_pdb2pqr() (in module gromacs_py.gromacs.tools.pdb2pqr)
concat_coor() (gromacs_py.gromacs.gmx5.GmxSys static method)
concat_edr() (gromacs_py.gromacs.gmx5.GmxSys method)
concat_pdb() (gromacs_py.gromacs.tools.pdb_manip.Coor static method)
concat_traj() (gromacs_py.gromacs.gmx5.GmxSys method)
convert_trj() (gromacs_py.gromacs.gmx5.GmxSys method)
Coor (class in gromacs_py.gromacs.tools.pdb_manip)
copy_box() (gromacs_py.gromacs.gmx5.GmxSys method)
correct_chain() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
correct_cys_name() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
correct_his_name() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
correct_water_name() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
create_and_go_dir() (in module gromacs_py.gromacs.tools.os_command)
create_box() (gromacs_py.gromacs.gmx5.GmxSys method)
create_dir() (in module gromacs_py.gromacs.tools.os_command)
create_peptide() (gromacs_py.gromacs.gmx5.GmxSys method)
cyclic_peptide_top() (gromacs_py.gromacs.gmx5.GmxSys method)
D
define_env() (gromacs_py.gromacs.tools.os_command.Command method)
del_atom_index() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
delete_directory() (in module gromacs_py.gromacs.tools.os_command)
delete_file() (in module gromacs_py.gromacs.tools.os_command)
display() (gromacs_py.gromacs.gmx5.GmxSys method)
(gromacs_py.gromacs.tools.os_command.Command method)
display_history() (gromacs_py.gromacs.gmx5.GmxSys method)
display_raw() (gromacs_py.gromacs.tools.os_command.Command method)
dist_under_index() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
E
em() (gromacs_py.gromacs.gmx5.GmxSys method)
em_2_steps() (gromacs_py.gromacs.gmx5.GmxSys method)
em_equi_three_step_iter_error() (gromacs_py.gromacs.gmx5.GmxSys method)
equi_three_step() (gromacs_py.gromacs.gmx5.GmxSys method)
extend_equi_prod() (gromacs_py.gromacs.gmx5.GmxSys method)
extract_log_dict() (in module gromacs_py.gromacs.tools.monitor)
F
full_path_and_check() (in module gromacs_py.gromacs.tools.os_command)
G
get_aa_num() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
get_aa_seq() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
get_all_output() (gromacs_py.gromacs.gmx5.GmxSys method)
get_attribute_selection() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
get_directory() (in module gromacs_py.gromacs.tools.os_command)
get_ener() (gromacs_py.gromacs.gmx5.GmxSys method)
get_gmx_version() (in module gromacs_py.gromacs.tools.os_command)
get_index_dist_between() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
get_index_selection() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
get_last_output() (gromacs_py.gromacs.gmx5.GmxSys method)
get_selection_index() (gromacs_py.gromacs.gmx5.TopMol method)
get_simulation_time() (gromacs_py.gromacs.gmx5.GmxSys method)
GmxSys (class in gromacs_py.gromacs.gmx5)
gromacs_py.gromacs.tools.monitor (module)
gromacs_py.gromacs.tools.os_command (module)
gromacs_py.gromacs.tools.pdb2pqr (module)
I
insert_mol() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
insert_mol_sys() (gromacs_py.gromacs.gmx5.GmxSys method)
is_exe() (in module gromacs_py.gromacs.tools.os_command)
isnotebook() (in module gromacs_py.gromacs.tools.monitor)
Itp (class in gromacs_py.gromacs.gmx5)
M
make_peptide() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
mol_num() (gromacs_py.gromacs.gmx5.TopSys method)
P
prepare_top() (gromacs_py.gromacs.gmx5.GmxSys method)
print_log_file() (in module gromacs_py.gromacs.tools.monitor)
production() (gromacs_py.gromacs.gmx5.GmxSys method)
prot_res_num() (gromacs_py.gromacs.gmx5.TopSys method)
R
read_pdb() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
run() (gromacs_py.gromacs.tools.os_command.Command method)
run_background() (gromacs_py.gromacs.tools.os_command.Command method)
run_md_sim() (gromacs_py.gromacs.gmx5.GmxSys method)
run_simulation() (gromacs_py.gromacs.gmx5.GmxSys method)
S
save_state() (gromacs_py.gromacs.gmx5.GmxSys method)
select_part_dict() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
simulation_plot() (in module gromacs_py.gromacs.tools.monitor)
solvate_add_ions() (gromacs_py.gromacs.gmx5.GmxSys method)
solvate_box() (gromacs_py.gromacs.gmx5.GmxSys method)
T
TopMol (class in gromacs_py.gromacs.gmx5)
TopSys (class in gromacs_py.gromacs.gmx5)
translate() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
W
water_to_ATOM() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
which() (in module gromacs_py.gromacs.tools.os_command)
write_pdb() (gromacs_py.gromacs.tools.pdb_manip.Coor method)
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